Evaluate gene sets identified by SDAN
Wei Sun
2024-07-10
Setup
Check enrichment of gene sets
Read in gene info and gene set assignments
file_tag = sprintf("%s_%s", cell_type_name, graph_weight)
assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = sapply(gene_sets, strsplit, split=",")
n_genes = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 7.00 22.00 26.00 24.57 28.25 30.00## [1] 40## [1] 7 14 15 17 19 21 21 21 21 22 22 23 23 23 24 25 25 26 26 26 26 26 26 26 27
## [26] 27 27 28 28 28 29 29 29 29 29 29 29 30 30 30Find gene symbols
Find gene symbols from bioMart.
All the gene symbols that can be found in bioMart are
consistent with what we have. So no need to run it.
ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
gene_BM = getBM(attributes = c("hgnc_symbol", "external_gene_name"),
filters = "external_gene_name",
values = assayed_genes,
mart = ensembl)
length(assayed_genes)
dim(gene_BM)
gene_BM[1:2,]
table(assayed_genes %in% gene_BM$external_gene_name)
t1 = table(gene_BM$external_gene_name)
dup = names(t1)[t1 > 1]
gene_BM[gene_BM$external_gene_name %in% dup,]
table(gene_BM$hgnc_symbol == gene_BM$external_gene_name)
w2kp = which(gene_BM$hgnc_symbol != gene_BM$external_gene_name)
gene_BM[w2kp,]Find gene symbols using the alias2Symbol function from
limma.
a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
gi = assayed_genes[i]
ai = alias2Symbol(gi)
if(length(ai) > 1){
print(gi)
print(ai)
}
a2s[i] = ai[1]
}
table(is.na(a2s))##
## FALSE TRUE
## 1739 261##
## FALSE TRUE <NA>
## 21 1718 261gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)
gene_info[sym_in_data != sym_limma,]## sym_in_data sym_limma
## 1: LRRC6 DNAAF11
## 2: C11orf49 CSTPP1
## 3: LINC00476 ERCC6L2-AS1
## 4: HNRNPA1P48 HNRNPA1L3
## 5: ZRANB2-AS2 ZRANB2-DT
## 6: LINC00271 AHI1-DT
## 7: RFX3-AS1 RFX3-DT
## 8: LINC00884 ATP13A3-DT
## 9: FBXO30-DT EPM2A-DT
## 10: LINC00894 EOLA2-DT
## 11: COX10-AS1 COX10-DT
## 12: LINC01184 SLC12A2-DT
## 13: FAM198B-AS1 GASK1B-AS1
## 14: C5orf17 LINC02899
## 15: C8orf37-AS1 CFAP418-AS1
## 16: LINC01146 HISLA
## 17: BTBD11 ABTB3
## 18: H2BU1 H2BC26
## 19: SKIV2L SKIC2
## 20: FAM155A NALF1
## 21: CTB-41I6.2 PIK3R5-DT
## sym_in_data sym_limmagene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma & (gene_symbol != "MT-CO2")),
gene_symbol := sym_limma]
dim(gene_info)## [1] 2000 3## sym_in_data sym_limma gene_symbol
## 1: CFTR CFTR CFTR
## 2: ICA1 ICA1 ICA1
## 3: PDK4 PDK4 PDK4
## 4: CALCR CALCR CALCR
## 5: ABCB4 ABCB4 ABCB4## t1
## 1
## 2000Prepare gene set information
Gene set annotations (by gene symbols) were downloaded from MSigDB website.
gmtfile = list()
gmtfile[["reactome"]] = "../Annotation/c2.cp.reactome.v2023.2.Hs.symbols.gmt"
gmtfile[["go_bp"]] = "../Annotation/c5.go.bp.v2023.2.Hs.symbols.gmt"
pathways = list()
for(k1 in names(gmtfile)){
pathways[[k1]] = gmtPathways(gmtfile[[k1]])
}
names(pathways)## [1] "reactome" "go_bp"## reactome go_bp
## 1692 7647Filter gene sets for size between 10 and 500.
## $reactome
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 7.0 9.0 12.0 17.0 23.0 31.0 44.0 71.8 120.9 1463.0
##
## $go_bp
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 6.0 8.0 10.0 14.0 19.0 29.0 46.0 80.8 183.0 1966.0Conduct enrichment analysis
## [1] 2000 3## sym_in_data sym_limma gene_symbol
## 1: CFTR CFTR CFTR
## 2: ICA1 ICA1 ICA1## [1] 36517 9## gene_ids feature_is_filtered feature_name feature_reference
## 1: ENSG00000000003 FALSE TSPAN6 NCBITaxon:9606
## 2: ENSG00000000005 FALSE TNMD NCBITaxon:9606
## feature_biotype n_cells_by_counts mean_counts pct_dropout_by_counts
## 1: gene 76 0.002350 99.8100
## 2: gene 1 0.000025 99.9975
## total_counts
## 1: 94
## 2: 1## [1] 2000##
## TRUE
## 2000##
## FALSE TRUE
## 34517 2000gene_dat$selected = 0
gene_dat$selected[match(gene_info$sym_in_data, gene_dat$feature_name)] = 1
table(gene_dat$selected)##
## 0 1
## 34517 2000## $`0`
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.00 94.48 99.58 93.53 99.97 100.00
##
## $`1`
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.6475 65.5944 84.3650 76.3053 93.6756 97.9950gene_info = merge(gene_info, gene_dat, by.x="sym_in_data",
by.y="feature_name", all.x = TRUE, all.y = FALSE)
dim(gene_info)## [1] 2000 12## sym_in_data sym_limma gene_symbol gene_ids feature_is_filtered
## 1: AATK AATK AATK ENSG00000181409 FALSE
## 2: ABAT ABAT ABAT ENSG00000183044 FALSE
## feature_reference feature_biotype n_cells_by_counts mean_counts
## 1: NCBITaxon:9606 gene 3157 0.091525
## 2: NCBITaxon:9606 gene 9074 0.368950
## pct_dropout_by_counts total_counts selected
## 1: 92.1075 3661 1
## 2: 77.3150 14758 1max_n2kp = 10
goseq_res = NULL
for(k in 1:length(gene_sets)){
if(length(gene_sets[[k]]) < 10) { next }
print(k)
set_k = paste0("set_", k)
print(gene_sets[[k]])
genes = gene_info$sym_in_data %in% gene_sets[[k]]
names(genes) = gene_info$gene_symbol
table(genes)
pwf = nullp(genes, "hg38", "geneSymbol",
bias.data = 100 - gene_info$pct_dropout_by_counts)
for(k1 in names(pathways)){
p1 = pathways[[k1]]
res1 = goseq(pwf, "hg38", "geneSymbol",
gene2cat=goseq:::reversemapping(p1))
res1$FDR = p.adjust(res1$over_represented_pvalue, method="BH")
nD = sum(res1$FDR < 0.05)
if(nD > 0){
res1 = res1[order(res1$FDR),][1:min(nD, max_n2kp),]
res1$category = gsub("REACTOME_|GOBP_", "", res1$category)
res1$category = gsub("_", " ", res1$category)
res1$category = tolower(res1$category)
res1$category = substr(res1$category, start=1, stop=81)
goseq_res[[set_k]][[k1]] = res1
}
}
}## [1] 1
## [1] "MCTP2" "ADAMTS3" "GHRL" "HESX1"
## [5] "UCN" "WDR25" "EYS" "PAPSS2"
## [9] "CARNMT1-AS1" "MTCP1" "LINC01277" "LINC00271"
## [13] "LINC02884" "RPL34-DT" "RP11-195C7.1" "KCNMA1-AS1"
## [17] "RP11-544A12.8" "STARD4-AS1" "C5orf17" "LINC02196"
## [21] "MIR100HG" "RP1-71H24.1" "LINC02444" "RP11-58G13.1"
## [25] "RP11-354K4.2" "TRG-AS1" "RP11-237N2.1" "RP11-314E10.1"
## [1] 2
## [1] "MTERF1" "PIGC" "ADAMTS19" "ADGRG5"
## [5] "BEX3" "FLJ40194" "TMEM151B" "PCED1B"
## [9] "H2BC4" "H2BC18" "COL5A2" "ENTPD3-AS1"
## [13] "TEX41" "ZNF451-AS1" "RP4-568F9.6" "RP11-557H15.4"
## [17] "LINC02642" "BDNF-AS" "LINC02057" "AC008697.1"
## [21] "CTD-2537O9.1" "RP11-370I10.6" "H2AC19" "H2BC8"
## [25] "H2AC8" "RP11-495L19.1" "RP11-321P16.3" "RP11-399K19.1"
## [1] 3
## [1] "SIGLEC1" "ADGRD1" "F13A1" "CH25H"
## [5] "TMEM44" "BANK1" "ADAMTS15" "ODF3B"
## [9] "RP11-445F6.2" "LINC01515" "AC002539.1" "RP3-525N10.2"
## [13] "AC007682.1" "RP11-142A5.1" "LINC02211" "FAM66D"
## [17] "OVCH1-AS1" "CTD-2336H13.2" "LINC02073" "CERNA2"
## [21] "LINC02885" "RP11-38B6.1"
## [1] 4
## [1] "APBB1IP" "ACER3" "PLEK" "TBC1D14" "NPL" "ARMH4"
## [7] "GAREM1" "RASGEF1C" "AOPEP" "DISP1" "DEPTOR" "ATF7IP2"
## [13] "MARCHF3" "DLEU1" "SLC8A1" "SCFD2" "PRKN" "MBD5"
## [19] "HMGA1P4" "XACT" "LINC01094" "RNASET2" "ARHGAP6" "PADI2"
## [25] "FMN1"
## [1] 5
## [1] "CELSR3" "GALNT16" "LILRB5" "HS3ST2"
## [5] "NRG2" "JAML" "PLPP3" "RANBP3L"
## [9] "FSTL5" "STXBP6" "HPSE2" "LRRC3B"
## [13] "ADGRB1" "VMO1" "POTEG" "ZNF521"
## [17] "FAM153CP" "FAM229A" "RP11-47I22.3" "AF064858.8"
## [21] "TRHDE-AS1" "AC002066.1" "RP11-696N14.1" "CPEB2-DT"
## [25] "SELENOP" "RP11-79E3.2" "RP11-661A12.5" "RP11-429A20.3"
## [29] "RP11-396B14.2" "RP11-436D23.1"
## [1] 6
## [1] "MMP24" "C4orf19" "CYTL1" "ENO4"
## [5] "FAM177B" "CLEC9A" "INSYN2B" "ANKUB1"
## [9] "ELMO1-AS1" "TMLHE-AS1" "ENTPD1-AS1" "AC096558.1"
## [13] "SRGAP2-AS1" "AC037445.1" "RP11-528G1.2" "DIAPH2-AS1"
## [17] "LINC01141" "MEF2C-AS2" "LINC02742" "RP11-649G15.2"
## [21] "RP11-452H21.1" "CTD-2647E9.3" "RP11-815J21.4" "ABHD15-AS1"
## [25] "RP11-16C1.3" "RP11-793A3.2" "CTD-3149D2.4" "CTD-2282P23.2"
## [29] "DISC2"
## [1] 7
## [1] "NAV3" "LY96" "FGGY" "ZDHHC14" "KCNQ3"
## [6] "MIR99AHG" "MEF2C-AS1" "LINC02232" "ATP6V0D1-DT" "KCNQ2"
## [11] "CUX2" "FRMD4B" "WDR45B" "SLC2A5" "HSPA12A"
## [16] "RBFOX3" "MYO1D" "KCNQ5" "ZNF846" "ZNF407"
## [21] "LNCAROD"
## [1] 8
## [1] "TENT5A" "CYREN" "TMEM241" "RALGPS1"
## [5] "SLC49A4" "GASK1A" "PUS10" "GASK1B"
## [9] "ACYP2" "RNLS" "LIPE-AS1" "ALOX12-AS1"
## [13] "HDAC2-AS2" "COX10-AS1" "MIR4300HG" "RP11-10H3.1"
## [17] "C8orf37-AS1" "RP11-554D14.6" "LINC02328" "RP11-187O7.3"
## [21] "MIR222HG" "RP11-323F24.5" "RP1-111C20.3" "RP11-574F11.4"
## [25] "ATOH8" "KLF13"
## [1] 9
## [1] "IFT43" "ATP5F1E" "STAB1" "LCP2" "HDHD5" "SESN1" "DOCK3"
## [8] "BICRAL" "GTDC1" "AFDN" "PRAM1" "CCDC40" "NR6A1" "RSU1"
## [15] "SLC2A13" "SH3RF1" "ST3GAL2" "NEK10" "PRKG1" "AIDA" "GLDN"
## [22] "PARVB" "IARS1"
## [1] 10
## [1] "SNCAIP" "PITPNM2" "PROCR" "IL1A" "C3" "FGF13"
## [7] "STON2" "RNF157" "KCNMB1" "KCNMA1" "TSPAN7" "TAGAP"
## [13] "RIC3" "P2RY12" "XIST" "LINC01091" "MMP28" "RGCC"
## [19] "SH3BP5" "LPL" "KCNE1"
## [1] 12
## [1] "OPHN1" "CASS4" "RIPOR2" "PDE10A" "PLCL1"
## [6] "AHI1" "WDPCP" "UNC80" "IRAK1BP1" "TENM4"
## [11] "CACNA1D" "SMIM14" "ZNF608" "CAPS2" "FIGN"
## [16] "RTN4RL1" "COL25A1" "PRDX6-AS1" "AC011288.2" "LINC00894"
## [21] "GMDS-DT" "RP11-673E1.1" "RP11-160E2.6" "RP4-681L3.3" "HIVEP2"
## [26] "MCTP1"
## [1] 13
## [1] "SLC1A3" "RAPGEF1" "PTPRE" "SSH2" "FER" "MGAT5"
## [7] "FMNL2" "CDC42SE2" "RUNX1" "CLASP2" "OXR1" "LDLRAD4"
## [13] "GPHN" "BNC2" "CHD2" "PACS1" "PCDH9" "PDE4B"
## [19] "NEAT1"
## [1] 14
## [1] "NIPAL2" "CPED1" "GPAT3" "SESN3"
## [5] "ARHGAP42" "CYSLTR1" "RAB39A" "CATSPERE"
## [9] "CDIN1" "SDHAF3" "MAMDC2-AS1" "FIRRE"
## [13] "CTA-292E10.6" "RP11-37B2.1" "RP11-630C16.2" "RP11-946L16.1"
## [17] "MIR223HG" "SNX25" "OGFRL1" "SEM1"
## [21] "RASGEF1B" "C17orf67" "CLEC5A"
## [1] 15
## [1] "SLC5A9" "RAB38" "CFAP74" "TCERG1L"
## [5] "SPDYE2" "RP11-165F24.3" "RP11-526K17.2" "HCG22"
## [9] "LINC00960" "RP11-712B9.2" "RP11-381K20.2" "RP11-39E3.3"
## [13] "RP11-434H14.1" "RP11-493L12.3" "RP11-317G6.1" "PRKCA-AS1"
## [17] "H2BC7" "RP11-622O11.6" "COL5A3" "SLC26A7"
## [21] "SNED1" "HTR1E" "DIRC3" "DARS1-AS1"
## [25] "CYP1B1-AS1" "AC092835.2" "MIR155HG" "RP11-384C4.7"
## [29] "LINC01138"
## [1] 16
## [1] "SYNDIG1" "FAM149A" "SPATA6" "C1QC"
## [5] "MIR31HG" "LINC01357" "FTCDNL1" "RP11-162D16.2"
## [9] "RP11-120D5.1" "LINC01684" "CEACAM16-AS1" "LINC00907"
## [13] "KCNQ1OT1" "RP11-74J13.8" "EIF1B-AS1" "RP11-437L7.2"
## [17] "RP11-685G11.1" "APBB3" "DARS1" "COL5A1"
## [21] "MFSD4B" "H2AC6" "ZC3H6" "CTD-2643I7.5"
## [25] "RP11-707P17.1" "RP11-452F19.4"
## [1] 17
## [1] "ZNF532" "ARHGEF18"
## [3] "PLAGL1" "FLVCR2"
## [5] "PUDP" "PCBD2"
## [7] "ARHGAP20" "SAMSN1"
## [9] "DENND2B" "CDYL2"
## [11] "SPTLC3" "MICOS10"
## [13] "PGBD5" "B3GLCT"
## [15] "TMSB4X" "LINC00630"
## [17] "RP11-535M15.1" "SLC16A1-AS1"
## [19] "LMCD1-AS1" "PVT1"
## [21] "LIX1-AS1" "LINC01605_ENSG00000253161"
## [23] "RP11-588H23.3" "LINC01146"
## [25] "RP11-281A20.2" "RP11-692P14.1"
## [27] "RP11-111G13.1"
## [1] 18
## [1] "PRKCQ" "PKD2L2" "ANGPT2" "MAP2K6" "NEK11" "PTPRB"
## [7] "FMO5" "PDE5A" "EFCAB11" "MED12L" "MTHFD2L" "TMEM52B"
## [13] "SLC35G2" "KCNMB2" "LTC4S" "KIF9-AS1" "CNTN1" "HGF"
## [19] "RASGRP2" "EMILIN2" "CRIM1" "CAMK4" "KCND3" "C11orf80"
## [25] "PPM1E" "NELL2"
## [1] 19
## [1] "LRRC7" "ARHGAP10" "RAPGEF4" "FGF14" "ADAM23"
## [6] "ATP8A2" "PDZD2" "STXBP5L" "PAM" "TENM2"
## [11] "ADGRL3" "NCAM2" "CSMD3" "NLGN1" "CTNND2"
## [16] "FUT9" "CADM2" "RIMS2" "NRXN1" "FLRT2"
## [21] "NRG3" "TAFA2" "LINC00632" "SNHG14" "RP11-384F7.2"
## [26] "IQCJ-SCHIP1"
## [1] 20
## [1] "SGCE" "C11orf65" "RP11-321C24.1" "ARHGAP26-AS1"
## [5] "ALG13-AS1" "RP11-353M9.1" "MYCBP2-AS1" "CCDC200"
## [9] "AC018890.6" "ZBTB20-AS5" "CTD-2015H6.3" "RP11-268P4.5"
## [13] "CTD-3239E11.2" "RP11-238K6.1" "RP11-513G19.1" "RP11-571M6.7"
## [17] "RP11-136F16.1" "RP11-713N11.4" "USP3-AS1" "RP11-16B9.1"
## [21] "RP11-106M3.3" "RNF213-AS1" "RP11-737O24.2" "RP11-53B2.3"
## [25] "RP4-769N13.7" "RP11-793H13.14" "RP11-458A7.1" "RP11-1146N6.3"
## [29] "RP11-685G9.5" "CTD-2021K4.2"
## [1] 21
## [1] "PER3" "CYFIP2" "DHRS9" "RPS6KA5" "STMN2" "ABCG2"
## [7] "SLC22A23" "PTPN14" "CCDC171" "PLEKHA7" "GAP43" "SVIL"
## [13] "LINC01278" "FOSL2" "SLC16A10" "CYTIP" "HIP1" "PARP8"
## [19] "SRSF12" "AGAP1" "FAM110B" "ZFPM2"
## [1] 22
## [1] "ANGPTL1" "ITGA9" "AGBL3" "LINC00539"
## [5] "AC017101.10" "RP1-225E12.2" "COA6-AS1" "AC083884.8"
## [9] "RP11-666F17.1" "DENND6A-AS1" "RP11-692D12.1" "RP11-679C8.2"
## [13] "RP11-703M24.5" "RP11-7F3.1" "AC009166.9" "ZFY"
## [17] "PXDNL" "RNF150" "LINC00910" "H1-0"
## [21] "KLF3-AS1" "LINC02646" "RP11-351A11.1" "HIF1A-AS3"
## [25] "RP11-322M13.1" "CTD-2285E13.1" "RP11-404C6.6"
## [1] 23
## [1] "NEURL2" "LILRB2"
## [3] "PEBP4" "IGSF11"
## [5] "ADGRA3" "LINC00467"
## [7] "SLC9B1" "H2AC20"
## [9] "FSIP2" "LINC01285"
## [11] "ATP6AP1L" "AC003090.1"
## [13] "RMDN2-AS1" "LINC01376"
## [15] "MEIKIN" "RP11-246A10.1"
## [17] "ALG1L9P_ENSG00000248671" "AC006160.5"
## [19] "RP11-1H15.2" "RP11-511B23.2"
## [21] "RP11-638I2.8" "LINC00639"
## [23] "RP11-221G19.1" "RP1-18C9.3"
## [25] "RP11-21M24.6" "RP11-65F13.4"
## [27] "RP11-56I23.2" "AMER2"
## [29] "LINC00970"
## [1] 24
## [1] "LINC00996" "SLC26A3"
## [3] "HELLS" "CHI3L1"
## [5] "LYPD5" "TNFRSF11B"
## [7] "LINC02397" "ARL17B"
## [9] "MYO16-AS1" "RP3-467L1.4"
## [11] "RP11-657O9.1" "RP11-13N12.1"
## [13] "MTRNR2L1" "RP11-81K2.1"
## [15] "SCARNA2_ENSG00000270066" "LINC00551"
## [17] "CH507-513H4.1"
## [1] 25
## [1] "PCSK1N" "IER3" "ARL5C" "AZIN2"
## [5] "NLGN4Y" "MIR4435-2HG" "GLIPR1L1" "TMEM72-AS1"
## [9] "RP1-30E17.2" "SLC8A1-AS1" "MIR646HG" "KCNMB2-AS1"
## [13] "ARHGAP8" "STX18-AS1" "ANK2-AS1" "RP11-281P23.2"
## [17] "ZFPM2-AS1" "MAILR" "AP000487.6" "RP11-516C1.1"
## [21] "LINC00621" "RP11-399K21.11" "LINC02712" "RP11-305E17.8"
## [25] "RP11-19D22.1" "RP11-264E23.4" "RP11-555K12.4" "PCDH11Y"
## [1] 26
## [1] "PEX7" "RAB40B" "ARAP2" "ABCA7"
## [5] "FAM107B" "SLC9A7" "RNMT" "IL4I1"
## [9] "DCUN1D4" "ZC4H2" "BTG1" "ADCY3"
## [13] "FAM117B" "COLEC12" "CCDC107" "FRMD5"
## [17] "RBM44" "ARL4C" "SYCP2" "H2BU1"
## [21] "CR1L" "CD247" "DENND1B" "AS3MT"
## [25] "USP2-AS1" "RP11-368L12.1"
## [1] 27
## [1] "P3H2" "AKAP7" "ACVR2A" "PLAU" "SMAD6"
## [6] "CCDC102B" "PRMT9" "SLC9A9" "KCNIP1" "DYNC2H1"
## [11] "HLA-DRA" "CYTH1" "AGAP3" "CSGALNACT1" "EVA1C"
## [1] 28
## [1] "RPL3" "RPL18A" "RPL19" "RPL34" "RPL24"
## [6] "LDAH" "RPS24" "RPS2" "RPS11" "RPL11"
## [11] "RPS27A" "RPL32" "RAB28" "RPL26" "RPL38"
## [16] "RPLP2" "RPS23" "RPL12" "RPL23A" "ZNF433-AS1"
## [21] "ADARB1"
## [1] 29
## [1] "MAP3K20" "ARRDC2" "CDH26" "KIAA0513"
## [5] "CCNG2" "PGGHG" "TIAM2" "AMN1"
## [9] "CFAP161" "ANKRD30BL" "MARCHF8" "PDZRN4"
## [13] "CXXC5" "LINC00862" "RP5-864K19.4" "SGO1-AS1"
## [17] "RP11-147G16.1" "RP11-154D17.1" "RP11-305L7.3" "SLC5A4-AS1"
## [21] "LINC01322" "RP11-20D14.3" "FMNL1-DT" "HCG17"
## [25] "RP11-154H23.4" "AC003099.2"
## [1] 30
## [1] "ST6GAL1" "FRMD4A" "SFMBT2" "DENND1A" "CHSY1" "DENND4C"
## [7] "TLR2" "SSBP2" "ARHGAP18" "JAK1" "RBM47" "AXL"
## [13] "TANC2" "TLR5"
## [1] 31
## [1] "PLPP1" "CARMIL1" "NME3" "PLGRKT" "TMEM156"
## [6] "MMS22L" "TMEM144" "FILIP1L" "SRGAP3" "LINC01356"
## [11] "PTCHD4" "ST3GAL1" "PDE8A" "PILRA" "RGS1"
## [16] "GRK3" "SRGN" "SEC14L1" "TMEM65" "ROBO1"
## [21] "CYRIA" "MIR181A1HG" "IFITM10"
## [1] 32
## [1] "TTC7A" "HAMP" "PIGL" "BTG2"
## [5] "LIPC" "MACROD2" "TTTY14" "DLEU7"
## [9] "LINC02649" "AC007879.5" "RP11-202G18.1" "CCDC26"
## [13] "RFX3-AS1" "LINC00884" "RNF217-AS1" "RP11-360F5.1"
## [17] "LINC02762" "CTC-575N7.1" "RP11-624C23.1" "RP11-463D19.1"
## [21] "SMIM35" "RP11-196H14.2" "RP11-323I15.5" "COPG2IT1"
## [1] 33
## [1] "KIF26B" "ADAM22" "PDE4A" "CELF4" "MOB3B" "TGFBI"
## [7] "PPFIA2" "CACNA1B" "ARID5B" "CACNA1C" "CACNA2D1" "FMN2"
## [13] "SORCS3" "SYN2" "GRM5" "GRIN1" "CADM1" "SYN3"
## [19] "MYT1L" "DPYD" "RYR2"
## [1] 34
## [1] "CALCR" "MBNL3" "ADGRG6" "PID1"
## [5] "NMNAT3" "BEAN1" "TMC7" "LINC00476"
## [9] "ARSJ" "SCOC-AS1" "AC105760.2" "ZRANB2-AS2"
## [13] "RP5-1198O20.4" "ITGA9-AS1" "RP11-634B7.4" "RORA-AS1"
## [17] "MIR3142HG" "LINC00506" "RP11-622I12.1" "RP11-1H15.4"
## [21] "RP11-6G22.1" "MAMLD1" "SPOCK2" "TBC1D10C"
## [25] "LINC01435" "RP1-179N16.6" "AGBL1"
## [1] 35
## [1] "CHD5" "OLFM1" "CEMIP2" "CBLN2"
## [5] "CDH18" "CNTN5" "NPAS3" "ME3"
## [9] "AK5" "PALM2AKAP2" "CLSTN2" "ABCG1"
## [13] "CAMK2N1" "LRFN5" "NEGR1" "RESF1"
## [17] "H1-10" "LSAMP" "PTPRT" "CACNA1E"
## [21] "TOX" "FAM155A" "MEG3" "RP11-191L9.4"
## [25] "MIAT" "SHISA9" "RP11-17A1.3" "RP11-259O2.1"
## [29] "RP11-111A21.1"
## [1] 36
## [1] "ATP8B1" "IL7" "SSPN" "SHOC1"
## [5] "PLD4" "AC002463.3" "HNRNPA1P48" "AC105461.1"
## [9] "RP11-142M10.2" "ARHGAP15-AS1" "RP5-1132H15.1" "LANCL1-AS1"
## [13] "RP11-575L7.8" "FBXO30-DT" "CPB2-AS1" "RP1-117O3.2"
## [17] "KDM4A-AS1" "BCL2L1-AS1" "RP11-544A12.4" "LRIG2-DT"
## [21] "RP11-775D22.3" "RHOQ-AS1" "RP11-506H20.1" "LMO7-AS1"
## [25] "RP11-66H6.3" "RP11-126O1.4" "RP1-256G22.2" "RP11-261A24.1"
## [29] "RP11-168F24.3" "RP11-13J12.3"
## [1] 37
## [1] "XKR6" "SKA2" "KIAA0825" "KATNAL1" "PRKAG2" "CLIP4"
## [7] "MXI1" "PATJ" "CLVS2" "ST18" "PITPNC1" "RASA2"
## [13] "ZFYVE28" "EDIL3" "DLGAP1" "JAKMIP2" "SAMD12" "CSMD1"
## [19] "OPCML" "RALYL" "KCNIP4" "SLIT1" "KAZN" "BASP1-AS1"
## [25] "SATB1-AS1"
## [1] 38
## [1] "ABCB4" "OMD" "ACKR4" "ADAMTS17"
## [5] "ABCA8" "GLT1D1" "FOLR2" "MT1E"
## [9] "RAB37" "MCMDC2" "RP11-131L23.1" "EDNRB-AS1"
## [13] "SMCR5" "AC073115.7" "AC092431.3" "KIF5C-AS1"
## [17] "AC073115.6" "RP5-1101C3.1" "CTB-161M19.4" "MTRNR2L8"
## [21] "RP11-867G2.8" "PRANCR" "PSMD7-DT" "TCF4-AS1"
## [25] "RP11-121C2.3" "RP11-413N10.3" "RP11-275G7.2" "RP11-4F5.3"
## [29] "GADD45B"
## [1] 39
## [1] "NEXMIF" "CRYM" "LRRC6" "CALY"
## [5] "DUOX1" "HERC6" "RNF180" "DOK6"
## [9] "TSBP1-AS1" "RP13-188A5.1" "PCDH9-AS2" "IPO9-AS1"
## [13] "RAP2C-AS1" "RP11-123B3.2" "RP11-120A1.1" "RP11-541P9.3"
## [17] "ZNF10" "RP11-493L12.4" "LINC02316" "CEROX1"
## [21] "ZNF528-AS1" "LINC02666" "RP11-314L11.1" "RP1-80B9.4"
## [25] "RP4-545L17.11" "RP11-320L2.1" "RP11-617F9.2" "LINC01762"
## [29] "SAP30-DT"
## [1] 40
## [1] "ZNF804B" "SYT7" "ADGRL1" "IGSF9B" "NALCN"
## [6] "KCNT1" "ARFGEF3" "DNAH6" "CSMD2" "ATP8A1"
## [11] "PCSK2" "GPNMB" "ZNF365" "BTBD11" "ZNF385D"
## [16] "SPOCK1" "FBXO32" "GABRB1" "PRICKLE2" "ARHGEF3"
## [21] "ADGRV1" "SRRM3" "TMTC2" "GPC5" "KCTD16"
## [26] "RORB" "CTC-340A15.2" "LINC01414" "CTC-535M15.2"
for(n1 in names(goseq_res)){
k = as.numeric(gsub("set_", "", n1))
print(n1)
print(gene_sets[[k]])
print(goseq_res[[n1]])
}## [1] "set_2"
## [1] "MTERF1" "PIGC" "ADAMTS19" "ADGRG5"
## [5] "BEX3" "FLJ40194" "TMEM151B" "PCED1B"
## [9] "H2BC4" "H2BC18" "COL5A2" "ENTPD3-AS1"
## [13] "TEX41" "ZNF451-AS1" "RP4-568F9.6" "RP11-557H15.4"
## [17] "LINC02642" "BDNF-AS" "LINC02057" "AC008697.1"
## [21] "CTD-2537O9.1" "RP11-370I10.6" "H2AC19" "H2BC8"
## [25] "H2AC8" "RP11-495L19.1" "RP11-321P16.3" "RP11-399K19.1"
## $reactome
## category
## 412 hats acetylate histones
## 415 hcmv late events
## 416 hdacs deacetylate histones
## 1164 ub specific processing proteases
## 413 hcmv early events
## 414 hcmv infection
## 147 chromatin modifying enzymes
## 226 deubiquitination
## 9 activated pkn1 stimulates transcription of ar androgen receptor regulated genes k
## 76 assembly of the orc complex at the origin of replication
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 412 2.965695e-08 1 5 9
## 415 5.778771e-08 1 5 11
## 416 6.316395e-08 1 5 11
## 1164 3.170673e-07 1 5 16
## 413 3.274704e-07 1 5 14
## 414 4.014105e-07 1 5 15
## 147 1.143854e-06 1 5 20
## 226 1.512997e-06 1 5 24
## 9 1.930756e-06 1 4 8
## 76 1.930756e-06 1 4 8
## FDR
## 412 2.488660e-05
## 415 2.488660e-05
## 416 2.488660e-05
## 1164 7.741401e-05
## 413 7.741401e-05
## 414 7.907787e-05
## 147 1.311299e-04
## 226 1.311299e-04
## 9 1.311299e-04
## 76 1.311299e-04
##
## [1] "set_7"
## [1] "NAV3" "LY96" "FGGY" "ZDHHC14" "KCNQ3"
## [6] "MIR99AHG" "MEF2C-AS1" "LINC02232" "ATP6V0D1-DT" "KCNQ2"
## [11] "CUX2" "FRMD4B" "WDR45B" "SLC2A5" "HSPA12A"
## [16] "RBFOX3" "MYO1D" "KCNQ5" "ZNF846" "ZNF407"
## [21] "LNCAROD"
## $reactome
## category over_represented_pvalue
## 1177 voltage gated potassium channels 1.791959e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 1177 0.9999999 3 7 0.02118095
##
## [1] "set_28"
## [1] "RPL3" "RPL18A" "RPL19" "RPL34" "RPL24"
## [6] "LDAH" "RPS24" "RPS2" "RPS11" "RPL11"
## [11] "RPS27A" "RPL32" "RAB28" "RPL26" "RPL38"
## [16] "RPLP2" "RPS23" "RPL12" "RPL23A" "ZNF433-AS1"
## [21] "ADARB1"
## $reactome
## category over_represented_pvalue
## 138 cellular response to starvation 0
## 301 eukaryotic translation elongation 0
## 302 eukaryotic translation initiation 0
## 452 influenza infection 0
## 557 metabolism of amino acids and derivatives 0
## 640 nonsense mediated decay nmd 0
## 801 regulation of expression of slits and robos 0
## 850 response of eif2ak4 gcn2 to amino acid deficiency 0
## 901 rrna processing 0
## 927 selenoamino acid metabolism 0
## under_represented_pvalue numDEInCat numInCat FDR
## 138 1 17 26 0
## 301 1 17 23 0
## 302 1 17 23 0
## 452 1 17 27 0
## 557 1 17 41 0
## 640 1 17 23 0
## 801 1 17 27 0
## 850 1 17 25 0
## 901 1 17 25 0
## 927 1 17 26 0
##
## $go_bp
## category over_represented_pvalue
## 630 cytoplasmic translation 0.000000e+00
## 4283 ribosome biogenesis 0.000000e+00
## 4279 ribosomal large subunit biogenesis 5.300278e-10
## 4278 ribosomal large subunit assembly 4.261838e-08
## 4281 ribosomal small subunit biogenesis 2.070857e-07
## 4282 ribosome assembly 2.095572e-07
## 3144 protein rna complex organization 7.898271e-06
## 2221 non membrane bounded organelle assembly 5.073840e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 630 1.0000000 17 23 0.000000e+00
## 4283 1.0000000 8 13 0.000000e+00
## 4279 1.0000000 5 5 8.339104e-07
## 4278 1.0000000 4 4 5.028969e-05
## 4281 1.0000000 4 5 1.648517e-04
## 4282 1.0000000 4 5 1.648517e-04
## 3144 0.9999999 4 10 5.325691e-03
## 2221 0.9999976 5 30 2.993565e-02
##
## [1] "set_33"
## [1] "KIF26B" "ADAM22" "PDE4A" "CELF4" "MOB3B" "TGFBI"
## [7] "PPFIA2" "CACNA1B" "ARID5B" "CACNA1C" "CACNA2D1" "FMN2"
## [13] "SORCS3" "SYN2" "GRM5" "GRIN1" "CADM1" "SYN3"
## [19] "MYT1L" "DPYD" "RYR2"
## $go_bp
## category over_represented_pvalue
## 280 calcium ion transport into cytosol 8.454614e-07
## under_represented_pvalue numDEInCat numInCat FDR
## 280 1 4 5 0.003990578Session information
## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 8955014 478.3 16112782 860.6 NA 16112782 860.6
## Vcells 16664170 127.2 31295066 238.8 65536 31295066 238.8## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] goseq_1.50.0 geneLenDataBase_1.34.0 BiasedUrn_2.0.10
## [4] fgsea_1.24.0 biomaRt_2.54.1 limma_3.54.2
## [7] tidyr_1.3.0 ggpubr_0.6.0 ggplot2_3.4.2
## [10] data.table_1.14.8
##
## loaded via a namespace (and not attached):
## [1] nlme_3.1-162 matrixStats_1.0.0
## [3] bitops_1.0-7 bit64_4.0.5
## [5] filelock_1.0.2 progress_1.2.2
## [7] httr_1.4.6 GenomeInfoDb_1.34.9
## [9] tools_4.2.3 backports_1.4.1
## [11] bslib_0.4.2 utf8_1.2.3
## [13] R6_2.5.1 mgcv_1.8-42
## [15] DBI_1.1.3 BiocGenerics_0.44.0
## [17] colorspace_2.1-0 withr_2.5.0
## [19] tidyselect_1.2.0 prettyunits_1.1.1
## [21] bit_4.0.5 curl_5.0.1
## [23] compiler_4.2.3 cli_3.6.1
## [25] Biobase_2.58.0 xml2_1.3.4
## [27] DelayedArray_0.24.0 rtracklayer_1.58.0
## [29] sass_0.4.5 scales_1.2.1
## [31] rappdirs_0.3.3 Rsamtools_2.14.0
## [33] stringr_1.5.0 digest_0.6.31
## [35] rmarkdown_2.21 XVector_0.38.0
## [37] pkgconfig_2.0.3 htmltools_0.5.5
## [39] MatrixGenerics_1.10.0 dbplyr_2.3.2
## [41] fastmap_1.1.1 rlang_1.1.0
## [43] rstudioapi_0.14 RSQLite_2.3.1
## [45] BiocIO_1.8.0 jquerylib_0.1.4
## [47] generics_0.1.3 jsonlite_1.8.4
## [49] BiocParallel_1.32.6 dplyr_1.1.2
## [51] car_3.1-2 RCurl_1.98-1.12
## [53] magrittr_2.0.3 GO.db_3.16.0
## [55] GenomeInfoDbData_1.2.9 Matrix_1.6-4
## [57] Rcpp_1.0.10 munsell_0.5.0
## [59] S4Vectors_0.36.2 fansi_1.0.4
## [61] abind_1.4-5 lifecycle_1.0.3
## [63] stringi_1.7.12 yaml_2.3.7
## [65] carData_3.0-5 SummarizedExperiment_1.28.0
## [67] zlibbioc_1.44.0 org.Hs.eg.db_3.16.0
## [69] BiocFileCache_2.6.1 grid_4.2.3
## [71] blob_1.2.4 parallel_4.2.3
## [73] crayon_1.5.2 lattice_0.20-45
## [75] splines_4.2.3 Biostrings_2.66.0
## [77] cowplot_1.1.1 GenomicFeatures_1.50.4
## [79] hms_1.1.3 KEGGREST_1.38.0
## [81] knitr_1.44 pillar_1.9.0
## [83] GenomicRanges_1.50.2 rjson_0.2.21
## [85] ggsignif_0.6.4 codetools_0.2-19
## [87] stats4_4.2.3 fastmatch_1.1-3
## [89] XML_3.99-0.14 glue_1.6.2
## [91] evaluate_0.20 png_0.1-8
## [93] vctrs_0.6.2 gtable_0.3.3
## [95] purrr_1.0.1 cachem_1.0.7
## [97] xfun_0.39 broom_1.0.4
## [99] restfulr_0.0.15 rstatix_0.7.2
## [101] tibble_3.2.1 GenomicAlignments_1.34.1
## [103] AnnotationDbi_1.60.2 memoise_2.0.1
## [105] IRanges_2.32.0